The destroyer USS Stethem passed less than 12 nautical miles (22 kilometres) from tiny Triton Island in the Paracel Islands archipelago, which is also claimed by Taiwan and Vietnam, the official told AFP.
The operation, which is likely to provoke Beijing, is the second of its kind carried out by the United States since President Donald Trump took office.
The first was on May 25, when the USS Dewey, a guided- missile destroyer, sailed less than 12 nautical miles from Mischief Reef -- part of the disputed Spratly Islands south of the Paracel Islands.
The United Nations says countries can establish the reach of their territorial waters up to a limit of 12 nautical miles.
China has rapidly built reefs into artificial islands capable of hosting military planes.
Freedom of navigation operations are designed to challenge the sovereignty of countries with claims to disputed territory. Washington has challenged annexations of South China Sea islets while advocating for a diplomatic settlement.
China has recently built up its facilities on Triton Island, including a new helicopter landing site, according to the Asia Maritime Transparency Initiative, part of the Center for Strategic and International Studies think tank.
According to the Pentagon, the United States in fiscal year 2016 conducted freedom of navigation operations "challenging excessive maritime claims of 22 different coastal states, including claims of allies and partners."
US-Chinese relations were already strained last week when Trump authorised a new arms sale to Taiwan, which China considers a rebel province, and when the US slapped sanctions on a Chinese bank accused of laundering North Korean cash.
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